Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 127 of 214
Found at i:38711592 original size:21 final size:21
Alignment explanation
Indices: 38711568--38711634 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
38711558 AAAAGTAAAA
38711568 TTTATAATTTTA-TCAAAAACT
1 TTTATAATTTTACT-AAAAACT
* *
38711589 TTTA-AATATTACTTAAAACT
1 TTTATAATTTTACTAAAAACT
*
38711609 TTAATAATTATTTACTAAAAA-T
1 TTTATAA-T-TTTACTAAAAACT
38711631 TTTA
1 TTTA
38711635 ATGAAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 15 0.42
21 7 0.19
22 5 0.14
23 9 0.25
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTATAATTTTACTAAAAACT
Found at i:38711629 original size:23 final size:22
Alignment explanation
Indices: 38711582--38711652 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
38711572 TAATTTTATC
38711582 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
38711602 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
* *
38711625 AAAAATTTTAATGAAA-ATTA-G
1 AAAAACTTTAAT-AAATATTACT
38711646 AAAAACT
1 AAAAACT
38711653 ATATATACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.20
21 6 0.15
22 8 0.20
23 16 0.40
24 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:38717141 original size:35 final size:35
Alignment explanation
Indices: 38717101--38717169 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
38717091 TTCAATTTTC
38717101 GAAAGTGATAATTTATCAGTCAATAGATACATTTA
1 GAAAGTGATAATTTATCAGTCAATAGATACATTTA
* *
38717136 GAAAGTGATAATTTATCATTCAATGGATACATTT
1 GAAAGTGATAATTTATCAGTCAATAGATACATTT
38717170 TCATGGGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (35 bp):
GAAAGTGATAATTTATCAGTCAATAGATACATTTA
Found at i:38725580 original size:20 final size:20
Alignment explanation
Indices: 38725557--38725609 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
38725547 ATATCCATAC
38725557 ATATTTTTATATACATATGT
1 ATATTTTTATATACATATGT
* * * *
38725577 ATATATGTATGTACTTATGT
1 ATATTTTTATATACATATGT
38725597 ATATTTTCTATAT
1 ATATTTT-TATAT
38725610 TTTATAATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATATTTTTATATACATATGT
Found at i:38725799 original size:33 final size:33
Alignment explanation
Indices: 38725700--38725805 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
38725690 ACCTATTCTA
* * *
38725700 TACTATCTCGGCGGACTTACTCTTTTTCGTGTT
1 TACTATCCCGACGGACTTACTCTGTTTCGTGTT
* ** *
38725733 TACTGTCCCGATAGACTTACTCTGTTTCATGTT
1 TACTATCCCGACGGACTTACTCTGTTTCGTGTT
38725766 TACTATCCCGACGGACTTACTCTG-TTCTGTGTT
1 TACTATCCCGACGGACTTACTCTGTTTC-GTGTT
*
38725799 TATTATC
1 TACTATC
38725806 TTGGTAGATT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 3 0.05
33 57 0.95
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (33 bp):
TACTATCCCGACGGACTTACTCTGTTTCGTGTT
Found at i:38730519 original size:33 final size:29
Alignment explanation
Indices: 38730474--38730534 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
38730464 TCAGCTTACC
*
38730474 GTTACACCGTTAACGGCTTAGTGACTAAAAT
1 GTTACACCGTTAAC-G-TAAGTGACTAAAAT
38730505 GTTACAACACGTTAACGTAAGTGACTAAAA
1 GTTAC-AC-CGTTAACGTAAGTGACTAAAA
38730535 CATAACACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 17 0.63
32 3 0.11
33 7 0.26
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (29 bp):
GTTACACCGTTAACGTAAGTGACTAAAAT
Found at i:38736338 original size:15 final size:15
Alignment explanation
Indices: 38736318--38736347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38736308 GAGATATGTT
38736318 GAAGCAGCAGCTTGG
1 GAAGCAGCAGCTTGG
*
38736333 GAAGCAGCGGCTTGG
1 GAAGCAGCAGCTTGG
38736348 ATTTCCTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.43, T:0.13
Consensus pattern (15 bp):
GAAGCAGCAGCTTGG
Found at i:38738228 original size:31 final size:32
Alignment explanation
Indices: 38738193--38738261 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
38738183 TTAAGAGCCA
* *
38738193 AATGACTT-AAATAAAAATTTTCGAATAATTC
1 AATGACTTGAAATAAAAACTTTCAAATAATTC
* *
38738224 AATGA-TTGAAATAAAAACTTTCAAATAGTTT
1 AATGACTTGAAATAAAAACTTTCAAATAATTC
38738255 AATGACT
1 AATGACT
38738262 ATTTTGTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 29 0.91
32 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (32 bp):
AATGACTTGAAATAAAAACTTTCAAATAATTC
Found at i:38742601 original size:44 final size:44
Alignment explanation
Indices: 38742514--38742627 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
38742504 CCAGTATGGG
*** * *
38742514 AAGACAAGATCTGCTTATTTTTTATCTACTTCATGCCAGTACATA
1 AAGACAAGATCTGCTT-TTTCCGATCTACTTCACGCCAATACATA
* *
38742559 AAGACAAGATCTG-TTTTCTCCGATCTACTTCACGTCAATACATG
1 AAGACAAGATCTGCTTTT-TCCGATCTACTTCACGCCAATACATA
38742603 AAGACAAGATCTGCTTTTTCCGATC
1 AAGACAAGATCTGCTTTTTCCGATC
38742628 GATTCCACTG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 2 0.03
44 41 0.68
45 17 0.28
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (44 bp):
AAGACAAGATCTGCTTTTTCCGATCTACTTCACGCCAATACATA
Found at i:38742922 original size:45 final size:45
Alignment explanation
Indices: 38742835--38743017 Score: 156
Period size: 45 Copynumber: 4.1 Consensus size: 45
38742825 GGACCTACTA
** * ** *
38742835 TCTTTGATCTGTTTCA-CACCGGTACATGAAAACAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTACGGGAAGACAAGATCTGCTT
* * * *
38742879 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTACGGGAAGACAAGATCTGCTT
* * * * * *
38742924 TCTTCGATCTACTCCACCACCTGTACGGGGAGACAAGATCTGGTA
1 TCTTTGATCTACTTCACCACCAGTACGGGAAGACAAGATCTGCTT
* * **
38742969 TCTATGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTG-TT
1 TCTTTGATCTACTTCACCACCAGTACGGGAAGACAAGATCTGCTT
38743012 ATCTTT
1 -TCTTT
38743018 CAACCTGCAC
Statistics
Matches: 109, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
43 1 0.01
44 38 0.35
45 70 0.64
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (45 bp):
TCTTTGATCTACTTCACCACCAGTACGGGAAGACAAGATCTGCTT
Found at i:38762728 original size:24 final size:25
Alignment explanation
Indices: 38762679--38762734 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
38762669 CCTATCTCAT
* * * *
38762679 TATATATATTTTTATAATTTTTATA
1 TATATATAATATTATAATTGTGATA
38762704 T-TATATAATATTATAATTGTGATA
1 TATATATAATATTATAATTGTGATA
38762728 TATATAT
1 TATATAT
38762735 GAGATGATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATATAATATTATAATTGTGATA
Found at i:38764041 original size:23 final size:23
Alignment explanation
Indices: 38764011--38764086 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
38764001 AGTGTTACTA
38764011 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
**
38764034 ATCAGTGGTAGCTAAGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
38764057 ATCAGTGGTAGCTTCGACTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
38764080 ATCAGTG
1 ATCAGTG
38764087 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38767871 original size:17 final size:17
Alignment explanation
Indices: 38767851--38767885 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38767841 TGGTCGTATG
38767851 TCACACACGCCCGTGTC
1 TCACACACGCCCGTGTC
* *
38767868 TCACACATGCTCGTGTC
1 TCACACACGCCCGTGTC
38767885 T
1 T
38767886 TAAGCCGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.40, G:0.17, T:0.26
Consensus pattern (17 bp):
TCACACACGCCCGTGTC
Found at i:38768620 original size:38 final size:38
Alignment explanation
Indices: 38768557--38768751 Score: 266
Period size: 38 Copynumber: 5.2 Consensus size: 38
38768547 AAATTTTAAT
* *
38768557 ACACTGGCAC-AAGCCTGCTAAGCACAGAGCCCGAATA
1 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
38768594 ACACTTGCACAAAGCCTGCTAGGCACATAGCCCGAATA
1 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
38768632 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
1 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* * *
38768670 TCACTGGCACAAAGCTTGCTAGGCATATAGCCCGAATA
1 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* *** *
38768708 TCACCAACACAAAGCCTGCTAGGCACATATCCCGAATA
1 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
38768746 TCACTG
1 ACACTG
38768752 CATTTCTATT
Statistics
Matches: 140, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
37 9 0.06
38 131 0.94
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (38 bp):
ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
Found at i:38770757 original size:15 final size:15
Alignment explanation
Indices: 38770737--38770766 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38770727 AGTGATAACA
38770737 TACAAATATTTTATT
1 TACAAATATTTTATT
38770752 TACAAATATTTTATT
1 TACAAATATTTTATT
38770767 GAGATTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TACAAATATTTTATT
Found at i:38777434 original size:24 final size:25
Alignment explanation
Indices: 38777407--38777475 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
38777397 TGCTCATACG
38777407 AGCTGTA-AACGGGAAGCTCCTCCA
1 AGCTGTATAACGGGAAGCTCCTCCA
* * * *
38777431 AGCTGAATAACGGGAAACTCGTGCA
1 AGCTGTATAACGGGAAGCTCCTCCA
* *
38777456 AGTTGTATAATGGGAAGCTC
1 AGCTGTATAACGGGAAGCTC
38777476 ATGCGAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
AGCTGTATAACGGGAAGCTCCTCCA
Found at i:38780662 original size:30 final size:31
Alignment explanation
Indices: 38780617--38780700 Score: 122
Period size: 30 Copynumber: 2.8 Consensus size: 31
38780607 TAACTCCTGT
*
38780617 ACTTTTC-AAATTTTACATTTTGACCCC-AA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
38780646 ACTTTTCTAAAATTTACATTTTGACCCCAAA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
*
38780677 AC-TTTCTAAAA-TTACATTTCGACC
1 ACTTTTCTAAAATTTACATTTTGACC
38780701 ATTAAAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 19 0.37
30 28 0.55
31 4 0.08
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (31 bp):
ACTTTTCTAAAATTTACATTTTGACCCCAAA
Found at i:38781337 original size:24 final size:24
Alignment explanation
Indices: 38781305--38781397 Score: 93
Period size: 24 Copynumber: 3.8 Consensus size: 24
38781295 GTGCGGCCCG
38781305 AAGAAGAAGAAAGAAGAAAGAAAA
1 AAGAAGAAGAAAGAAGAAAGAAAA
38781329 AAGAAGAAGAAA-AAGGGAGAAGAAAA
1 AAGAAGAAGAAAGAA--GA-AAGAAAA
*
38781355 GGAGAA-AAGAAAGAGAGAAAG-AAA
1 -AAGAAGAAGAAAGA-AGAAAGAAAA
* *
38781379 AAGAAAAAGAAAAAAGAAA
1 AAGAAGAAGAAAGAAGAAA
38781398 AAATTTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
23 11 0.19
24 22 0.37
25 5 0.08
26 15 0.25
27 5 0.08
28 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAGAAGAAGAAAGAAGAAAGAAAA
Found at i:38781397 original size:7 final size:7
Alignment explanation
Indices: 38781308--38781400 Score: 53
Period size: 7 Copynumber: 12.3 Consensus size: 7
38781298 CGGCCCGAAG
*
38781308 AAGAAGA
1 AAGAAAA
*
38781315 AAGAAGA
1 AAGAAAA
38781322 AAGAAAA
1 AAGAAAA
*
38781329 AAG-AAG
1 AAGAAAA
38781335 AAGAAAA
1 AAGAAAA
38781342 AGGGAGAAGAA
1 A---AGAA-AA
*
38781353 AAGGAGAA
1 AA-GAAAA
38781361 AAGAAAGA
1 AAGAAA-A
*
38781369 GAGAAAGA
1 AAGAAA-A
*
38781377 AAAAGAAA
1 AAGA-AAA
38781385 AAGAAAA
1 AAGAAAA
38781392 AAGAAAA
1 AAGAAAA
38781399 AA
1 AA
38781401 TTTAAAAGTC
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.07
7 34 0.49
8 19 0.28
9 4 0.06
10 4 0.06
11 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:38781397 original size:13 final size:13
Alignment explanation
Indices: 38781308--38781399 Score: 73
Period size: 13 Copynumber: 7.2 Consensus size: 13
38781298 CGGCCCGAAG
*
38781308 AAGAAGAAAGAAGA
1 AAGAAAAAAGAA-A
*
38781322 AAGAAAAAAGAAG
1 AAGAAAAAAGAAA
* * *
38781335 AAGAAAAAGGGAG
1 AAGAAAAAAGAAA
*
38781348 AAG-AAAAGGAGAA
1 AAGAAAAAAGA-AA
* *
38781361 AAG-AAAGAGAGA
1 AAGAAAAAAGAAA
38781373 AAG-AAAAAGAAA
1 AAGAAAAAAGAAA
38781385 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
38781398 AA
1 AA
38781400 ATTTAAAAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
12 20 0.31
13 34 0.52
14 11 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:38781806 original size:15 final size:16
Alignment explanation
Indices: 38781788--38781817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38781778 TAATTTAGTT
38781788 TTATTT-ATTTAAATA
1 TTATTTCATTTAAATA
38781803 TTATTTCATTTAAAT
1 TTATTTCATTTAAAT
38781818 TTAATTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTCATTTAAATA
Found at i:38782328 original size:17 final size:17
Alignment explanation
Indices: 38782308--38782357 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
38782298 AAAAAAATTA
*
38782308 TGTTTTCAAAACTTTCG
1 TGTTTTCAAAATTTTCG
*
38782325 TGTTTTCAAAATTTTTG
1 TGTTTTCAAAATTTTCG
38782342 TGTTTTCAAAATTTTC
1 TGTTTTCAAAATTTTC
38782358 ATGTGTTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:38782393 original size:21 final size:20
Alignment explanation
Indices: 38782367--38782434 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
38782357 CATGTGTTCG
38782367 TGTTTTCAAAAAAAATTCTCA
1 TGTTTTCAAAAAAAATT-TCA
**
38782388 TGTTTTTTAAAAAAATTTCA
1 TGTTTTCAAAAAAAATTTCA
38782408 TG-TTT-AAAAAAAA--TCA
1 TGTTTTCAAAAAAAATTTCA
38782424 TGTTTTCAAAA
1 TGTTTTCAAAA
38782435 TTTTCTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.12
17 3 0.07
18 11 0.26
19 3 0.07
20 5 0.12
21 15 0.36
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (20 bp):
TGTTTTCAAAAAAAATTTCA
Found at i:38782419 original size:20 final size:21
Alignment explanation
Indices: 38782374--38782420 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
38782364 TCGTGTTTTC
**
38782374 AAAAAAAATTCTCATGTTTTT
1 AAAAAAAATTCTCATGTTTAA
*
38782395 TAAAAAAATT-TCATGTTTAA
1 AAAAAAAATTCTCATGTTTAA
38782415 AAAAAA
1 AAAAAA
38782421 TCATGTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAAAAAATTCTCATGTTTAA
Found at i:38782434 original size:17 final size:18
Alignment explanation
Indices: 38782367--38782434 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 18
38782357 CATGTGTTCG
38782367 TGTTTTCAAAAAAAATTCTCA
1 TGTTTT-AAAAAAAA-T-TCA
*
38782388 TGTTTTTTAAAAAAATTTCA
1 TG--TTTTAAAAAAAATTCA
38782408 TG-TTTAAAAAAAA-TCA
1 TGTTTTAAAAAAAATTCA
38782424 TGTTTTCAAAA
1 TGTTTT-AAAA
38782435 TTTTCTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.12
17 13 0.32
18 4 0.10
20 5 0.12
21 3 0.07
22 7 0.17
23 4 0.10
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (18 bp):
TGTTTTAAAAAAAATTCA
Found at i:38782526 original size:20 final size:21
Alignment explanation
Indices: 38782486--38782525 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38782476 TCTATCGAAA
*
38782486 ATTTCCGTGTTTTCAAAAAAT
1 ATTTCCGCGTTTTCAAAAAAT
*
38782507 ATTTCCGCGTTTCCAAAAA
1 ATTTCCGCGTTTTCAAAAA
38782526 TTCAGGTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTTCCGCGTTTTCAAAAAAT
Found at i:38782560 original size:18 final size:17
Alignment explanation
Indices: 38782539--38782633 Score: 66
Period size: 18 Copynumber: 5.4 Consensus size: 17
38782529 AGGTGATTTA
38782539 AAAAATCGTCGTGTTTTC
1 AAAAATC-TCGTGTTTTC
**
38782557 AAAAA-CTCCAGTTTTC
1 AAAAATCTCGTGTTTTC
* * *
38782573 AAAATTTTCATGTTTTTC
1 AAAAATCTCGTG-TTTTC
*
38782591 AAAAAATTCTCGTGTTTTA
1 -AAAAA-TCTCGTGTTTTC
* *
38782610 AAAAATTTTCGTGTTCTC
1 AAAAA-TCTCGTGTTTTC
38782628 AAAAAT
1 AAAAAT
38782634 AAAAAATGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
16 12 0.20
17 5 0.08
18 30 0.50
19 8 0.13
20 5 0.08
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (17 bp):
AAAAATCTCGTGTTTTC
Found at i:38782598 original size:20 final size:19
Alignment explanation
Indices: 38782573--38782624 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
38782563 TCCAGTTTTC
*
38782573 AAAATTTTCATGTTTTTCAA
1 AAAATTTTCGTGTTTTT-AA
*
38782593 AAAATTCTCGTG-TTTTAA
1 AAAATTTTCGTGTTTTTAA
38782611 AAAATTTTCGTGTT
1 AAAATTTTCGTGTT
38782625 CTCAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.46
19 5 0.18
20 10 0.36
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAATTTTCGTGTTTTTAA
Found at i:38788008 original size:11 final size:11
Alignment explanation
Indices: 38787994--38788033 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
38787984 AAAAGAGAGA
38787994 AAAAAAACAAC
1 AAAAAAACAAC
*
38788005 AAAAAAATAAC
1 AAAAAAACAAC
**
38788016 AAAAAAGGAAC
1 AAAAAAACAAC
38788027 AAAAAAA
1 AAAAAAA
38788034 ACAAAGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.82, C:0.10, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:38788054 original size:34 final size:34
Alignment explanation
Indices: 38787978--38788054 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
38787968 TATTATACCT
*
38787978 GAAAAAAAAAGAGAGAAAAAAAACAACAAAAAAA
1 GAAAAAAAAAGAGACAAAAAAAACAACAAAAAAA
* *
38788012 TAACAAAAAAG-GAACAAAAAAAACAA-AGCAAAAAA
1 GAAAAAAAAAGAG-ACAAAAAAAACAACA--AAAAAA
38788047 GAAAAAAA
1 GAAAAAAA
38788055 CAAAGAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.06
34 21 0.60
35 12 0.34
ACGTcount: A:0.81, C:0.08, G:0.10, T:0.01
Consensus pattern (34 bp):
GAAAAAAAAAGAGACAAAAAAAACAACAAAAAAA
Found at i:38788064 original size:25 final size:24
Alignment explanation
Indices: 38787996--38788075 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 24
38787986 AAGAGAGAAA
*
38787996 AAAAACAACAAAAAAATAACAAAAAAGG
1 AAAAA-AAC-AAAAAA-AGCAAAAAA-G
*
38788024 AACAAAAA-AAACAAAGCAAAAAAG
1 AA-AAAAACAAAAAAAGCAAAAAAG
38788048 AAAAAAACAAAGAAAAG--AAAAAG
1 AAAAAAACAAA-AAAAGCAAAAAAG
38788071 AAAAA
1 AAAAA
38788076 TCAAGATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
23 16 0.35
24 6 0.13
25 12 0.26
26 5 0.11
28 4 0.09
29 3 0.07
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.01
Consensus pattern (24 bp):
AAAAAAACAAAAAAAGCAAAAAAG
Found at i:38788074 original size:20 final size:20
Alignment explanation
Indices: 38788007--38788066 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
38787997 AAAACAACAA
*
38788007 AAAAATAACAAA-AAAGGAAC
1 AAAAA-AACAAAGAAAAGAAC
*
38788027 AAAAAAAACAAAGCAAAA-AAG
1 -AAAAAAACAAAG-AAAAGAAC
38788048 AAAAAAACAAAGAAAAGAA
1 AAAAAAACAAAGAAAAGAA
38788067 AAAGAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.12
20 20 0.59
21 7 0.21
22 3 0.09
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (20 bp):
AAAAAAACAAAGAAAAGAAC
Found at i:38789043 original size:76 final size:76
Alignment explanation
Indices: 38788953--38790468 Score: 1954
Period size: 76 Copynumber: 19.6 Consensus size: 76
38788943 TTTCTGTTTT
* *
38788953 TTTTTC-AAATATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
38789017 TTTAAATTTCTG
65 TTTAAATTTCTG
38789029 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
*
38789093 TTTAAATTTCCG
65 TTTAAATTTCTG
38789105 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
*
38789169 TTTAAATTTTTG
65 TTTAAATTTCTG
* *
38789181 TTTTTCAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGT-T
1 TTTTTC---AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
*
38789245 TTTTTTTAATTTCTG
62 TTTTTTAAATTTCTG
* *
38789260 TTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 --TTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTA-T
38789325 TTTTTTAAATTTCTG
62 TTTTTTAAATTTCTG
* * *
38789340 CTTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
38789405 TTTTAATTTAATTTCTG
64 TTTT-A---AATTTCTG
* * *
38789422 TTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTATTT
1 -TTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
38789487 TTTT-AATTTCTG
64 TTTTAAATTTCTG
* * *
38789499 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTATTTT
1 -TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTT
*
38789564 TTT-AATTTCTAT
65 TTTAAATTTCT-G
* *
38789576 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTTT
*
38789641 TTTAATTTCTG
66 TTAAATTTCTG
* * *
38789652 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTA-TT
*
38789717 TTTTTTAATTTCTG
63 TTTTTAAATTTCTG
* * * ** *
38789731 CTTTTTTCAAAAAATCAGCTCATAATACAGAGGTGAGTTGAGCCTCAGGTCACGTTGAGGTGTTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
*
38789796 TTTTTAATTTCTG
64 TTTTAAATTTCTG
* *
38789809 TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
38789874 TTTTAAATTTCTG
64 TTTTAAATTTCTG
*
38789887 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGATCATGCCGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
**
38789952 CTTTTAAATTTCCA
64 -TTTTAAATTTCTG
*
38789966 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
38790030 TTTAAATTTCTG
65 TTTAAATTTCTG
38790042 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
*
38790106 TTTAAATTTCCG
65 TTTAAATTTCTG
*
38790118 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGTTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-T
38790182 TTTAAATTTCTG
65 TTTAAATTTCTG
* * * * **
38790194 TTTTTC-AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTGGACCATGCCGAGGTATTTC
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT-
*
38790258 TTTTAAATTTCTA
64 TTTTAAATTTCTG
* *
38790271 TTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA--TT
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTT
*
38790333 TTTCAA-TTCATG
65 TTTAAATTTC-TG
* ** * *
38790345 TTTTTC-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTA--
1 TTTTTCAAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTC-GGG-TCATGCCGAGGTATT
** *
38790407 -TTTTCGATTTTTG
63 TTTTTAAATTTCTG
* * * *
38790420 TTTTTC-GAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
38790469 GCACGCCGAG
Statistics
Matches: 1337, Mismatches: 76, Indels: 57
0.91 0.05 0.04
Matches are distributed among these distances:
73 4 0.00
74 50 0.04
75 49 0.04
76 536 0.40
77 127 0.09
78 247 0.18
79 169 0.13
80 43 0.03
81 45 0.03
82 67 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (76 bp):
TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTTT
TTAAATTTCTG
Found at i:38790722 original size:30 final size:31
Alignment explanation
Indices: 38790677--38790761 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 31
38790667 TAACCCTTTT
*
38790677 ACTTTTC-AAATTTTACATTTTGACCCC-AA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
38790706 ACTTTTCTAAAATTTACATTTTGACCCCAAA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
*
38790737 AC-TTTCTAAAA-TTACATTTTAACCC
1 ACTTTTCTAAAATTTACATTTTGACCC
38790762 TTAGACTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.38
30 28 0.54
31 4 0.08
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (31 bp):
ACTTTTCTAAAATTTACATTTTGACCCCAAA
Found at i:38790770 original size:60 final size:59
Alignment explanation
Indices: 38790689--38790816 Score: 136
Period size: 59 Copynumber: 2.2 Consensus size: 59
38790679 TTTTCAAATT
* * *
38790689 TTACATTTTGACCCCAAACTTT-TCTAAAATTTACATTTTGACCCCAAAACT-TTCTA-AAA
1 TTACATTTTAACCCCAAACTTTCTC-AAAA-TTACACTTTGACCCCAAAACTCTT-AAGAAA
* * * *
38790748 TTACATTTTAACCCTTAGACTTTCTCAAAATTGCACTTTGACCCCTAAACTCTTAAGAAA
1 TTACATTTTAACCC-CAAACTTTCTCAAAATTACACTTTGACCCCAAAACTCTTAAGAAA
38790808 TTACATTTT
1 TTACATTTT
38790817 GGCCCATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
59 32 0.55
60 24 0.41
61 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (59 bp):
TTACATTTTAACCCCAAACTTTCTCAAAATTACACTTTGACCCCAAAACTCTTAAGAAA
Found at i:38790778 original size:30 final size:29
Alignment explanation
Indices: 38790662--38790816 Score: 107
Period size: 30 Copynumber: 5.2 Consensus size: 29
38790652 ATTTTTTTTG
** *
38790662 CATTTTAACCCTTTTACTTTTCAAATTTTA
1 CATTTTAACCCTTAAACTTTTCAAA-ATTA
* *
38790692 CATTTTGACCC-CAAACTTTTCTAAAATTTA
1 CATTTTAACCCTTAAACTTTTC-AAAA-TTA
* **
38790722 CATTTTGACCCCAAAAC-TTTCTAAAATTA
1 CATTTTAACCCTTAAACTTTTC-AAAATTA
* *
38790751 CATTTTAACCCTTAGACTTTCTCAAAATTG
1 CATTTTAACCCTTAAACTTT-TCAAAATTA
* * * * *
38790781 CACTTTGACCCCTAAACTCTTAAGAAATTA
1 CATTTTAACCCTTAAACTTTTCA-AAATTA
38790811 CATTTT
1 CATTTT
38790817 GGCCCATATT
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
29 25 0.25
30 69 0.69
31 6 0.06
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
CATTTTAACCCTTAAACTTTTCAAAATTA
Found at i:38791398 original size:13 final size:13
Alignment explanation
Indices: 38791365--38791453 Score: 78
Period size: 13 Copynumber: 6.9 Consensus size: 13
38791355 GTGCAGCCCA
*
38791365 AAGAAGAAGAAAG
1 AAGAAGAAAAAAG
38791378 AAGAAAGAAAAAAG
1 AAG-AAGAAAAAAG
*
38791392 AAGAAGAAAAAGG
1 AAGAAGAAAAAAG
* *
38791405 GAGAAGAAAAGGAG
1 AAGAAGAAAA-AAG
38791419 AA-AAG-AAAAAG
1 AAGAAGAAAAAAG
38791430 -AGAA-AGAAAAAG
1 AAGAAGA-AAAAAG
*
38791442 AAAAAGAAAAAA
1 AAGAAGAAAAAA
38791454 AATTAAAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 1 0.02
11 4 0.07
12 9 0.15
13 32 0.52
14 15 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAAG
Found at i:38791428 original size:38 final size:37
Alignment explanation
Indices: 38791369--38791441 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 37
38791359 AGCCCAAAGA
38791369 AGAAGAAAGAAGAAAGAAAAAAGA-AGAAGAAAAAGGG
1 AGAAGAAAGAAGAAAGAAAAAAGAGA-AAGAAAAAGGG
*
38791406 AGAAGAAAAGGAGAAA-AGAAAAAGAGAAAGAAAAAG
1 AGAAG-AAAGAAGAAAGA-AAAAAGAGAAAGAAAAAG
38791442 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 6 0.19
38 25 0.78
39 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (37 bp):
AGAAGAAAGAAGAAAGAAAAAAGAGAAAGAAAAAGGG
Found at i:38791430 original size:6 final size:6
Alignment explanation
Indices: 38791364--38791452 Score: 81
Period size: 6 Copynumber: 14.5 Consensus size: 6
38791354 GGTGCAGCCC
* * * * *
38791364 AAAGAA GAAGAA AGAAGAA AGA-AA AAAGAA GAAGAA AAAGGGA GAAGAA
1 AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA
* *
38791413 AAGGAGA AAAGAA AAAGAG AAAGAA AAAGAA AAAGAA AAA
1 AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
38791453 AAATTAAAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
5 4 0.06
6 46 0.71
7 15 0.23
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:38791789 original size:11 final size:12
Alignment explanation
Indices: 38791771--38791800 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
38791761 CATCCAGCAG
38791771 AGAAAAGAAAAA
1 AGAAAAGAAAAA
38791783 A-AAAAGAAAAA
1 AGAAAAGAAAAA
38791794 AGAAAAG
1 AGAAAAG
38791801 GGCCCACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:38791873 original size:15 final size:16
Alignment explanation
Indices: 38791853--38791882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38791843 TTAATTAGTT
38791853 TTATTT-ATTTAAATA
1 TTATTTCATTTAAATA
38791868 TTATTTCATTTAAAT
1 TTATTTCATTTAAAT
38791883 TTAATTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTCATTTAAATA
Found at i:38792417 original size:17 final size:17
Alignment explanation
Indices: 38792372--38792417 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
38792362 AACAAAATTA
*
38792372 TGTTTTCAAAACTTTCG
1 TGTTTTCAAAATTTTCG
*
38792389 TGTTTTCAAAATTTTTG
1 TGTTTTCAAAATTTTCG
38792406 TGTTTTCAAAAT
1 TGTTTTCAAAAT
38792418 ATTCATGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:38792499 original size:18 final size:19
Alignment explanation
Indices: 38792431--38792499 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
38792421 CATGTGTTCG
38792431 TGTTTTCAAAAAAATTCTCA
1 TGTTTTCAAAAAAATT-TCA
* *
38792451 TGTTTTTTAAAAAAATTTCG
1 TG-TTTTCAAAAAAATTTCA
* *
38792471 TG-TTTAAAAAAAAATTCA
1 TGTTTTCAAAAAAATTTCA
38792489 TGTTTTCAAAA
1 TGTTTTCAAAA
38792500 TTTTCTTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 15 0.37
19 7 0.17
20 6 0.15
21 13 0.32
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (19 bp):
TGTTTTCAAAAAAATTTCA
Found at i:38792572 original size:21 final size:21
Alignment explanation
Indices: 38792548--38792590 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38792538 TCATCTATCG
* *
38792548 AAAATTTCCGTGTTTTCAAAA
1 AAAATTTCCGCGTTTCCAAAA
38792569 AAAATTTCCGCGTTTCCAAAA
1 AAAATTTCCGCGTTTCCAAAA
38792590 A
1 A
38792591 TTCAGGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATTTCCGCGTTTCCAAAA
Found at i:38792625 original size:18 final size:17
Alignment explanation
Indices: 38792604--38792698 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 17
38792594 AGGTGATTTA
38792604 AAAAATCGTCGTGTTTTC
1 AAAAATC-TCGTGTTTTC
38792622 AAAAA-CTCCG-GTTTTC
1 AAAAATCT-CGTGTTTTC
* * *
38792638 AAAATTTTCATGTTTTTC
1 AAAAATCTCGTG-TTTTC
*
38792656 AAAAAATTCTCGTGTTTTA
1 -AAAAA-TCTCGTGTTTTC
* *
38792675 AAAAATTTTCGTGTTCTC
1 AAAAA-TCTCGTGTTTTC
38792693 AAAAAT
1 AAAAAT
38792699 AAAAAATGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.20
17 6 0.10
18 30 0.49
19 8 0.13
20 5 0.08
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAAATCTCGTGTTTTC
Found at i:38792663 original size:20 final size:19
Alignment explanation
Indices: 38792638--38792689 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
38792628 TCCGGTTTTC
*
38792638 AAAATTTTCATGTTTTTCAA
1 AAAATTTTCGTGTTTTT-AA
*
38792658 AAAATTCTCGTG-TTTTAA
1 AAAATTTTCGTGTTTTTAA
38792676 AAAATTTTCGTGTT
1 AAAATTTTCGTGTT
38792690 CTCAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.46
19 5 0.18
20 10 0.36
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAATTTTCGTGTTTTTAA
Found at i:38796618 original size:38 final size:38
Alignment explanation
Indices: 38796560--38797015 Score: 572
Period size: 38 Copynumber: 12.0 Consensus size: 38
38796550 ATTTTCAAAA
* * * *
38796560 CACCGGCAC-AAGCCTACTAGGCACAGAGCCCGGATAA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* *
38796597 CACCGGTACAAAGCCTGCTAGGCACATAGCCCAAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* *
38796635 CACCGGTACAAAGCCTACTAGGCACATAGCCCGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* *
38796673 CACCGGCATAAAGCCTGCTAGGCACATAACCCGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
38796711 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* * * * *
38796749 CACCGTCACAAAGCCTGCTAGGCACAGAGCTCAAATAA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* *
38796787 CATCGGTACAAAGCCTGCTAGGCACATAGCCCGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* * * * *
38796825 CACTGGTACAAAGCCTGCTAGGCATATATCCTGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* * *
38796863 CACTGGCACAAAGCCTGCTAAGCACATATCCCGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* * * * *
38796901 GACCAGCACAAATCCTGCTAGGCACAAAGCCCAAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* * *
38796939 CACCGGCACAAAGCCTGCTAGGCACAGAGCTCGAATAA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
* ** *
38796977 CATCGATACAAAGCCTGCTAGGCACATAGCCTGAATAT
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
38797015 C
1 C
38797016 GCCACATTTC
Statistics
Matches: 361, Mismatches: 57, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
37 8 0.02
38 353 0.98
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (38 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATAT
Found at i:38803563 original size:21 final size:20
Alignment explanation
Indices: 38803539--38803585 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38803529 TAACACAATA
* *
38803539 TCAATTATTTTTAATTTTTTT
1 TCAATTA-TCTTAATTTTGTT
38803560 TCAATTATCTTAATTTTGTT
1 TCAATTATCTTAATTTTGTT
38803580 T-AATTA
1 TCAATTA
38803586 AGTTATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (20 bp):
TCAATTATCTTAATTTTGTT
Found at i:38806176 original size:20 final size:20
Alignment explanation
Indices: 38806092--38806178 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 20
38806082 TAGTATTTTT
*
38806092 TTAATTTAATATTAAAGTGA
1 TTAATTTAATATTAAATTGA
*
38806112 TT-ATCTTAATATCAAA-T--
1 TTAAT-TTAATATTAAATTGA
* * *
38806129 TTAATCTAATATATATCATTATA
1 TTAATTTAATAT-TA-AATT-GA
38806152 TTAATTTAATATTAAATTGA
1 TTAATTTAATATTAAATTGA
38806172 TTAATTT
1 TTAATTT
38806179 TAATCATATT
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
17 8 0.15
18 3 0.06
19 4 0.08
20 21 0.40
21 3 0.06
22 2 0.04
23 11 0.21
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (20 bp):
TTAATTTAATATTAAATTGA
Found at i:38813659 original size:14 final size:14
Alignment explanation
Indices: 38813640--38813814 Score: 74
Period size: 14 Copynumber: 12.3 Consensus size: 14
38813630 TATCACTATA
*
38813640 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
38813654 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
38813668 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
38813682 GTTTAGAAGTTACTAT-
1 GTTTAG-GGTT--TATG
*
38813698 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
* *
38813711 GATTATGGGTTTAGG
1 GTTTA-GGGTTTATG
* * *
38813726 GGTTATGATTTATG
1 GTTTAGGGTTTATG
* *
38813740 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* *
38813755 G-TTGGGGTTTAAG
1 GTTTAGGGTTTATG
*
38813768 GTTTAGAGGGTATAT-
1 GTTT--AGGGTTTATG
*
38813783 G-TTAGGAGTTTAGG
1 GTTTAGG-GTTTATG
38813797 GTTTTAGGGTTTA-G
1 G-TTTAGGGTTTATG
38813811 GTTT
1 GTTT
38813815 TAAGGTTTAG
Statistics
Matches: 122, Mismatches: 25, Indels: 29
0.69 0.14 0.16
Matches are distributed among these distances:
12 6 0.05
13 11 0.09
14 64 0.52
15 28 0.23
16 11 0.09
17 2 0.02
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:38813744 original size:7 final size:7
Alignment explanation
Indices: 38813698--38813751 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
38813688 AAGTTACTAT
*
38813698 TTTAAGG
1 TTTATGG
38813705 TTTATGG
1 TTTATGG
*
38813712 ATTATGGG
1 TTTAT-GG
*
38813720 TTTAGGG
1 TTTATGG
* *
38813727 GTTATGA
1 TTTATGG
38813734 TTTATGG
1 TTTATGG
38813741 TTTATGG
1 TTTATGG
38813748 TTTA
1 TTTA
38813752 AAGGTTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:38813815 original size:14 final size:14
Alignment explanation
Indices: 38813784--38813829 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
38813774 AGGGTATATG
38813784 TTAGGAGTTTAGGGTT
1 TTAGG-GTTTA-GGTT
38813800 TTAGGGTTTAGGTT
1 TTAGGGTTTAGGTT
*
38813814 TTAAGGTTTAGAGTT
1 TTAGGGTTTAG-GTT
38813829 T
1 T
38813830 AAAAGGTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 14 0.50
15 9 0.32
16 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTAGGTT
Found at i:38813830 original size:14 final size:14
Alignment explanation
Indices: 38813790--38813852 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
38813780 TATGTTAGGA
*
38813790 GTTTAGGGTTTTAGG
1 GTTTA-GGTTTTAAG
38813805 GTTTAGGTTTTAAG
1 GTTTAGGTTTTAAG
*
38813819 GTTTAGAGTTTAAAAG
1 GTTTAG-GTTT-TAAG
* *
38813835 G-TCAGGGTTTAAG
1 GTTTAGGTTTTAAG
38813848 GTTTA
1 GTTTA
38813853 AAGGTTATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
13 4 0.10
14 19 0.49
15 12 0.31
16 4 0.10
ACGTcount: A:0.24, C:0.02, G:0.32, T:0.43
Consensus pattern (14 bp):
GTTTAGGTTTTAAG
Found at i:38813866 original size:80 final size:79
Alignment explanation
Indices: 38813720--38813906 Score: 216
Period size: 80 Copynumber: 2.3 Consensus size: 79
38813710 GGATTATGGG
* * * ** *
38813720 TTTAGGGGTTATGATTTATGGTTTATG-GTTTAAAGGTTGGGGTTTAAGGTTTAGAGGGTATATG
1 TTTAGGGTTTAAGATTTAAGGTTTA-GAGTTTAAAGGTCAGGGTTTAAGGTTTAAAGGGTATATG
*
38813784 TT-AGGAGTTTAGGGT
65 TTAAGGA-TTTAGGAT
* * * *
38813799 TTTAGGGTTTAGGTTTTAAGGTTTAGAGTTTAAAAGGTCAGGGTTTAAGGTTTAAAGGTTATGTG
1 TTTAGGGTTTAAGATTTAAGGTTTAGAGTTT-AAAGGTCAGGGTTTAAGGTTTAAAGGGTATATG
38813864 TTAAGGATTTAGGAT
65 TTAAGGATTTAGGAT
*
38813879 TTTAGGGTTTTAAGATTTAGGGTTTAGA
1 TTTAGGG-TTTAAGATTTAAGGTTTAGA
38813907 TTAACTAGTG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 25 0.27
80 44 0.48
81 21 0.23
ACGTcount: A:0.25, C:0.01, G:0.32, T:0.43
Consensus pattern (79 bp):
TTTAGGGTTTAAGATTTAAGGTTTAGAGTTTAAAGGTCAGGGTTTAAGGTTTAAAGGGTATATGT
TAAGGATTTAGGAT
Found at i:38818039 original size:21 final size:21
Alignment explanation
Indices: 38818013--38818055 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
38818003 AGGACTCGGG
38818013 TCTTTAAAGTTCCTCAATCAT
1 TCTTTAAAGTTCCTCAATCAT
38818034 TCTTTAAAGTTCCTCAATCAT
1 TCTTTAAAGTTCCTCAATCAT
38818055 T
1 T
38818056 TTCTTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (21 bp):
TCTTTAAAGTTCCTCAATCAT
Found at i:38818438 original size:43 final size:43
Alignment explanation
Indices: 38818353--38818443 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
38818343 CTTTGAGTTC
* * * * *
38818353 ATTA-CAAGATTTTCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAAAGCATGATATCTTTT
* *
38818395 ATTACCAAGATTTACTTGATTAAGAAAAAGCATGGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAAAGCATGATATCTTTT
38818438 ATTACC
1 ATTACC
38818444 TTGCATATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.10
43 37 0.90
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAAAGCATGATATCTTTT
Found at i:38819077 original size:71 final size:71
Alignment explanation
Indices: 38818958--38819100 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
38818948 CACTCTACCT
* * *
38818958 ATATTCACTATTGAATAAATTTGTTAAAACTAACGTCGATAATGGTAATATAGAATAATAACAGA
1 ATATTCACTATTGAATAAATTTGTTAAAACTAACGTCAATAATGGTAATATAGAACAATAACAAA
38819023 ACAGAA
66 ACAGAA
* *
38819029 ATATTCACTATTGAATAAATTTGTTAAAACTAACGTCAATAATTGTAATATTGAACAATAACAAA
1 ATATTCACTATTGAATAAATTTGTTAAAACTAACGTCAATAATGGTAATATAGAACAATAACAAA
38819094 ACAGAA
66 ACAGAA
38819100 A
1 A
38819101 GAAAAGAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (71 bp):
ATATTCACTATTGAATAAATTTGTTAAAACTAACGTCAATAATGGTAATATAGAACAATAACAAA
ACAGAA
Found at i:38820152 original size:16 final size:16
Alignment explanation
Indices: 38820131--38820162 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38820121 AAAAATATTT
38820131 TTAAAAAATAAAAAAA
1 TTAAAAAATAAAAAAA
*
38820147 TTAAAAATTAAAAAAA
1 TTAAAAAATAAAAAAA
38820163 AATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
TTAAAAAATAAAAAAA
Found at i:38820161 original size:18 final size:20
Alignment explanation
Indices: 38820140--38820182 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38820130 TTTAAAAAAT
38820140 AAAAAAA-T-TAAAAATTAA
1 AAAAAAATTATAAAAATTAA
*
38820158 AAAAAAATTATAAAAATTCA
1 AAAAAAATTATAAAAATTAA
38820178 AAAAA
1 AAAAA
38820183 CTAGCACGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAAATTATAAAAATTAA
Found at i:38820163 original size:20 final size:22
Alignment explanation
Indices: 38820135--38820182 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
38820125 ATATTTTTAA
38820135 AAAATAAAAAAAT-TAAAAATT-
1 AAAA-AAAAAAATATAAAAATTC
*
38820156 -AAAAAAAAATTATAAAAATTC
1 AAAAAAAAAAATATAAAAATTC
38820177 AAAAAA
1 AAAAAA
38820183 CTAGCACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
22 5 0.22
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAAAAAAATATAAAAATTC
Found at i:38821768 original size:20 final size:19
Alignment explanation
Indices: 38821715--38821775 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
38821705 CCGAATTATA
38821715 TATTAAATATATAT-TTTT
1 TATTAAATATATATATTTT
* * *
38821733 ATTTTTAATCAAATATACTTTT
1 -TATTAAAT-ATATATA-TTTT
38821755 TATTAAATATATATATTTT
1 TATTAAATATATATATTTT
38821774 TA
1 TA
38821776 GACTTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 12 0.36
20 11 0.33
21 6 0.18
22 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTAAATATATATATTTT
Found at i:38821808 original size:41 final size:39
Alignment explanation
Indices: 38821706--38821825 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 39
38821696 TGGCCCGGCC
*
38821706 CGAATTATATATT-AA-ATATATATTTTT-ATTTTTAAT
1 CGAATTATATATTAAATATATATATTTTTAACTTTTAAT
* *
38821742 CAAATATACTTTTTATTAAATATATATATTTTTAGACTTTTAAT
1 CGAAT-TA---TATATTAAATATATATATTTTTA-ACTTTTAAT
*
38821786 ACGAATTATATATTAAATATATATATTTTT-ATTTTTAAT
1 -CGAATTATATATTAAATATATATATTTTTAACTTTTAAT
38821825 C
1 C
38821826 AAATATGGGC
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 1 0.01
39 8 0.12
40 5 0.07
41 23 0.33
42 12 0.17
44 10 0.14
45 4 0.06
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (39 bp):
CGAATTATATATTAAATATATATATTTTTAACTTTTAAT
Found at i:38823023 original size:56 final size:56
Alignment explanation
Indices: 38822959--38823945 Score: 700
Period size: 55 Copynumber: 17.7 Consensus size: 56
38822949 ACTGGTATAC
* * *
38822959 AAAAAAATTTGGGGTGCTGGCCTGTTAATGGTCGGCACCACCAGTACGAAAACAAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * * *
38823015 AAAAAAA-TTTGGATGTTGGCCTGTCAATGG-C--CAGCACCAGTATGAAAATGAAAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAA--CAAA
* * * * * **
38823069 AAATAAAATTTTTTTCGGCGCCGGCTTGTCAATGGCCGG---CACCAGTATG-AAACCGA
1 AAA-AAAA---TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * ** **
38823125 AAAAAAATTTTGGGTGCTAGCCTGTCAATGGCTGACACCACCAGTATAAAAACGGA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
*
38823181 AAAAAAATTTCT--GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC--G
1 AAAAAAATTT-TGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * * *
38823234 AAAAAAATTTTAGGTGCTGGCCTGTAAATGGCTGACACCACCAGTACAAAAACAAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * * *
38823290 AAAAAAATTTTGGGTGATGCCCTGTCAATGGTCGGCACCACCAATACGAAAA-AGGA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACA-AA
* * * **
38823346 AAAAAAATTTTGGGTGCTAGCCTGTAAATAG-TTG-A-CACCAGTACGAAAACAGAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACA-AA
* * * * * *
38823400 AAAAAAA-TTTGGGTGCTAGCTTATCAATGGCTGGCACCATCAGTACGAAAAC-GA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * * * *
38823454 AAAAATATTTTAGGTACTAGCCTGTCAATGGCCGGCACCACTAGTAGGAAAAC-AA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * * * * **
38823509 AAAAAAA-TTTGGGTGCTGGCCTGTAAATGGTCGACACCATCAGTACAAAAATGAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * **
38823564 AAAAAAA--TTGGGTGAC-GTCCTGTCAATGGCCGACACCACCAGTACGAAAA-AGGG
1 AAAAAAATTTTGGGTG-CTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACA-AA
* * * * *
38823618 AAAAAAATTTTGGGTGCTGACATATAAATGGCC-G-A-CACCAGTACGAAAAC-GA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
** * * * * * *
38823670 AAAAAAATTTTGCCTGCTTGCCTGTTAATGGCTGACATCACCAGTACGAAAACGGAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAA
* * ** * *
38823727 AAAAAAATTTTGGGTGTTGGCTTGTTGGCTTATCAATGGTTGGCACCATCAGTACGAAAACGAA
1 AAAAAAATTTT-GG-G-T-GC----TGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* * ** *
38823791 AAAAATATTTTAGGTATTGGCCTGTCAATGGCCGGCACTACCAGTACGAAAACGAAA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAA
* * * ** * * *
38823848 AAAAATATTTTTTTTGGTACTGGCCTGTCAATGGCCAACACCATCAGTATGAAAATAAA
1 AAAAA-A--ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
* *
38823907 AAAAAAA-ATTGGGTGCTAGCCTGTCAATGGCCGGCACCA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCA
38823946 AATTTATCAA
Statistics
Matches: 736, Mismatches: 146, Indels: 99
0.75 0.15 0.10
Matches are distributed among these distances:
52 63 0.09
53 56 0.08
54 142 0.19
55 170 0.23
56 159 0.22
57 20 0.03
58 5 0.01
59 35 0.05
60 40 0.05
61 3 0.00
62 1 0.00
63 1 0.00
64 13 0.02
65 28 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (56 bp):
AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAA
Found at i:38823267 original size:109 final size:110
Alignment explanation
Indices: 38822959--38823937 Score: 752
Period size: 109 Copynumber: 8.8 Consensus size: 110
38822949 ACTGGTATAC
* * * *
38822959 AAAAAAATTTGGGGTGCTGGCCTGTTAATGGTCGGCACCACCAGTACGAAAACAAAAAAAAAATT
1 AAAAAAATTT-GGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTT
* * * *
38823024 T-GGATGTTGGCCTGTCAATGGC---CAGCACCAGTATGAAAATGAAAA
65 TAGG-TGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACG--AA
* * * * * *
38823069 AAATAAAATTTTTTTCGGCGCCGGCTTGTCAATGGCCGG---CACCAGTATGAAACCGAAAAAAA
1 AAA-AAAA----TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAA
* * ** *
38823131 ATTTTGGGTGCTAGCCTGTCAATGGCTGACACCACCAGTATAAAAACGGA
61 ATTTTAGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACGAA
**
38823181 AAAAAAATTTCTGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACG-AAAAAAATTTT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTT
* * *
38823245 AGGTGCTGGCCTGTAAATGGCTGACACCACCAGTACAAAAACAAA
66 AGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACGAA
* * * * *
38823290 AAAAAAATTTTGGGTGATGCCCTGTCAATGGTCGGCACCACCAATACGAAAAAGGAAAAAAAATT
1 AAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG-AAAACGAAAAAAAATT
* * * * *
38823355 TTGGGTGCTAGCCTGTAAATAGTTG--A-CACCAGTACGAAAACAGAA
64 TTAGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAAC-GAA
* * * * * *
38823400 AAAAAAATTTGGGTGCTAGCTTATCAATGGCTGGCACCATCAGTACGAAAACGAAAAAATATTTT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTT
* * * * * *
38823465 AGGTACTAGCCTGTCAATGGCCGGCACCACTAGTAGGAAAAC-AA
66 AGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACGAA
* * * * * * *
38823509 AAAAAAATTTGGGTGCTGGCCTGTAAATGGTCGACACCATCAGTACAAAAATGAAAAAAAA-ATT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTT
* * * * *
38823573 GGGTGAC-GTCCTGTCAATGGCCGACACCACCAGTACGAAAAAGGGA
66 AGGTG-CTGGCCTGTCAATGGCTGACACCACCAGTACG-AAAACGAA
* * * * *
38823619 AAAAAATTTTGGGTGCTGACATATAAATGGCC-G-A-CACCAGTACGAAAACGAAAAAAAATTTT
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTT
* * * *
38823681 -GCCTGCTTGCCTGTTAATGGCTGACATCACCAGTACGAAAACGGAA
66 AG-GTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAAC-GAA
* * ** *
38823727 AAAAAAATTTTGGGTGTTGGCTTGTTGGCTTATCAATGGTTGGCACCATCAGTACGAAAACGAAA
1 AAAAAAA-TTT-GG-G-T-GC----TGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAA
** * * *
38823792 AAAATATTTTAGGTATTGGCCTGTCAATGGCCGGCACTACCAGTACGAAAACGAA
57 AAAA-ATTTTAGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACGAA
* * ** * * **
38823847 AAAAAATATTTTTTTTGGTACTGGCCTGTCAATGGCCAACACCATCAGTATGAAAATAAAAAAAA
1 AAAAAA-A----TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAA
** * *
38823912 AAATTGGGTGCTAGCCTGTCAATGGC
61 ATTTTAGGTGCTGGCCTGTCAATGGC
38823938 CGGCACCAAA
Statistics
Matches: 694, Mismatches: 131, Indels: 83
0.76 0.14 0.09
Matches are distributed among these distances:
107 50 0.07
108 101 0.15
109 163 0.23
110 92 0.13
111 67 0.10
112 37 0.05
113 2 0.00
114 34 0.05
115 23 0.03
116 35 0.05
117 11 0.02
118 1 0.00
119 1 0.00
120 32 0.05
121 38 0.05
122 2 0.00
123 1 0.00
124 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (110 bp):
AAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTT
AGGTGCTGGCCTGTCAATGGCTGACACCACCAGTACGAAAACGAA
Found at i:38825611 original size:21 final size:22
Alignment explanation
Indices: 38825587--38825627 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
38825577 AAGTTAAATT
*
38825587 TAAATTCA-AAAATAATATAAA
1 TAAATTCAGAAAAAAATATAAA
*
38825608 TAAATTGAGAAAAAAATATA
1 TAAATTCAGAAAAAAATATA
38825628 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
TAAATTCAGAAAAAAATATAAA
Found at i:38825713 original size:11 final size:11
Alignment explanation
Indices: 38825634--38825713 Score: 56
Period size: 11 Copynumber: 7.3 Consensus size: 11
38825624 TATATTTTTT
38825634 AAATGAAATGA
1 AAATGAAATGA
** *
38825645 AAGGGAAATGG
1 AAATGAAATGA
* *
38825656 TAATGGTAATGA
1 AAAT-GAAATGA
*
38825668 AAATGAAATTA
1 AAATGAAATGA
*
38825679 GAATGAAATGA
1 AAATGAAATGA
*
38825690 AACA-AAAAT-A
1 AA-ATGAAATGA
38825700 AAATGAAATGA
1 AAATGAAATGA
38825711 AAA
1 AAA
38825714 AAAGAAGTTC
Statistics
Matches: 49, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
9 1 0.02
10 7 0.14
11 32 0.65
12 9 0.18
ACGTcount: A:0.60, C:0.01, G:0.20, T:0.19
Consensus pattern (11 bp):
AAATGAAATGA
Found at i:38825713 original size:16 final size:16
Alignment explanation
Indices: 38825667--38825714 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
38825657 AATGGTAATG
* *
38825667 AAAATGAAATTAGAAT
1 AAAATGAAATAAAAAT
* *
38825683 GAAATGAAACAAAAAT
1 AAAATGAAATAAAAAT
38825699 AAAATGAAATGAAAAA
1 AAAATGAAAT-AAAAA
38825715 AAGAAGTTCG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (16 bp):
AAAATGAAATAAAAAT
Found at i:38830109 original size:108 final size:105
Alignment explanation
Indices: 38829885--38830138 Score: 275
Period size: 108 Copynumber: 2.4 Consensus size: 105
38829875 AAACTCAGCA
* * * *
38829885 CCAAATTTTTTTTTTCGTTTTCATACTGGTGGTGCCGACCATTGACAGGCCAGCACAAAAAAAAA
1 CCAAATTTTTTTTCT-GTTTTCGTACTGGTAGTGCCGACCATTGACAAGCCAGCACAAAAAAAAA
* *
38829950 TTTGTTTCCGTACTGGTGTCGGCCATTGATAGCCCAGCACC
65 TTTGTTTCCGTACTGGTGTCGGCCATTGACAGACCAGCACC
* * * * ****
38829991 CAAAAATTTTTTTCTGTTTTCGTACTGGTAGTGCCGGCCATTGACAAGCGAGCACCCAAAATTTT
1 CCAAATTTTTTTTCTGTTTTCGTACTGGTAGTGCCGACCATTGACAAGCCAGCA--CAAAAAAAA
* *
38830056 TTTTCGTTTTCGTACTGGTGTTC-GCCATTGACAGACCAGCACC
64 ATTT-GTTTCCGTACTGGTG-TCGGCCATTGACAGACCAGCACC
*
38830099 CCAAATTTTTTTTC-GTTTTCGTGCT-G--GTGCCGACCATTGA
1 CCAAATTTTTTTTCTGTTTTCGTACTGGTAGTGCCGACCATTGA
38830139 TAGGCTAGTA
Statistics
Matches: 124, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
104 13 0.10
105 34 0.27
106 13 0.10
107 18 0.15
108 44 0.35
109 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (105 bp):
CCAAATTTTTTTTCTGTTTTCGTACTGGTAGTGCCGACCATTGACAAGCCAGCACAAAAAAAAAT
TTGTTTCCGTACTGGTGTCGGCCATTGACAGACCAGCACC
Found at i:38830164 original size:52 final size:52
Alignment explanation
Indices: 38829893--38830156 Score: 230
Period size: 52 Copynumber: 5.0 Consensus size: 52
38829883 CACCAAATTT
*
38829893 TTTTTTTCGTTTTCATACTGGTGGTGCCGACCATTGACAGGCCAGCA--CAAAAA
1 TTTTTTTCGTTTTCGTAC---TGGTGCCGACCATTGACAGGCCAGCACCCAAAAA
**** * * * * *
38829946 AAAATTT-GTTTCCGTACTGGTGTCGGCCATTGATAGCCCAGCACCCAAAAA
1 TTTTTTTCGTTTTCGTACTGGTGCCGACCATTGACAGGCCAGCACCCAAAAA
* * * *
38829997 TTTTTTTCTGTTTTCGTACTGGTAGTGCCGGCCATTGACAAGCGAGCACCCAAAAT
1 TTTTTTTC-GTTTTCGTACT-G--GTGCCGACCATTGACAGGCCAGCACCCAAAAA
* * * *
38830053 TTTTTTTCGTTTTCGTACTGGTGTTCG-CCATTGACAGACCAGCACCCCAAAT
1 TTTTTTTCGTTTTCGTACTGGTG-CCGACCATTGACAGGCCAGCACCCAAAAA
* * * *
38830105 TTTTTTTCGTTTTCGTGCTGGTGCCGACCATTGATAGGCTAGTACCCAAAAA
1 TTTTTTTCGTTTTCGTACTGGTGCCGACCATTGACAGGCCAGCACCCAAAAA
38830157 AAATTTTCAT
Statistics
Matches: 168, Mismatches: 34, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
49 22 0.13
51 11 0.07
52 73 0.43
53 15 0.09
54 2 0.01
55 11 0.07
56 34 0.20
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (52 bp):
TTTTTTTCGTTTTCGTACTGGTGCCGACCATTGACAGGCCAGCACCCAAAAA
Found at i:38830375 original size:53 final size:52
Alignment explanation
Indices: 38830265--38830413 Score: 144
Period size: 52 Copynumber: 2.9 Consensus size: 52
38830255 GTTTTAGTGT
* * * * * * *
38830265 TGGTGCCAGCTATTGACAGGCCAGCGCTCAAATTTTTTTTTGTTTTCAAAAG
1 TGGTGCCACCCATTGACAGACAAGCACCCAAATTTTTTTTTATTTTCAAAAG
** *
38830317 TGGTGCCGA-CCATTGACACGACAA-CACCCAAATTTTTTTTTCATTTTCCTAGG
1 TGGTGCC-ACCCATTGACA-GACAAGCACCCAAATTTTTTTTT-ATTTTCAAAAG
*
38830370 TGGTGCCACCCATTGACAGGCAAGCACCC-AA-TTTTTTTTATTTT
1 TGGTGCCACCCATTGACAGACAAGCACCCAAATTTTTTTTTATTTT
38830414 TTTTTGTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
50 5 0.06
51 8 0.10
52 37 0.45
53 32 0.39
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (52 bp):
TGGTGCCACCCATTGACAGACAAGCACCCAAATTTTTTTTTATTTTCAAAAG
Found at i:38836537 original size:20 final size:18
Alignment explanation
Indices: 38836504--38836554 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 18
38836494 TCACACCAAT
*
38836504 AAATAATTTAAAAACTATAA
1 AAATATTTTAAAAA--ATAA
38836524 AAATATTTTTAAAAAATAA
1 AAATA-TTTTAAAAAATAA
38836543 AAA-ATTTTAAAA
1 AAATATTTTAAAA
38836555 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 1 0.03
19 7 0.24
20 5 0.17
21 8 0.28
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATTTTAAAAAATAA
Found at i:38838653 original size:3 final size:3
Alignment explanation
Indices: 38838645--38838675 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
38838635 GTCCCCTCTA
38838645 TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
38838676 AAAAACTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38845167 original size:46 final size:45
Alignment explanation
Indices: 38845092--38845194 Score: 172
Period size: 46 Copynumber: 2.3 Consensus size: 45
38845082 TACGTATGAT
* *
38845092 CACTTATCAC-TTGTCCCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
38845136 CACTTATCACTTTGTCACTAGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACT-GATCAGATAAGTGTAGCTAAAGCTAC
38845182 CACTTATCACTTT
1 CACTTATCACTTT
38845195 ATCTTTTGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 10 0.18
45 7 0.13
46 38 0.69
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:38845206 original size:46 final size:46
Alignment explanation
Indices: 38845092--38845208 Score: 157
Period size: 46 Copynumber: 2.6 Consensus size: 46
38845082 TACGTATGAT
* * *
38845092 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
38845136 CACTTATCACTTTGTCACTAGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTAC
**
38845182 CACTTATCACTTTATCTTTTGATCAGA
1 CACTTATCACTTTATCACTTGATCAGA
38845209 AGTACTCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 10 0.16
45 5 0.08
46 49 0.77
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:38850293 original size:23 final size:22
Alignment explanation
Indices: 38850262--38850304 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
38850252 CTTAATTCCT
*
38850262 TCAAAAATGATCAAATTATAAA
1 TCAAAAATGATAAAATTATAAA
38850284 TCAATAAATGATAAAATTATA
1 TCAA-AAATGATAAAATTATA
38850305 TTTTGATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
TCAAAAATGATAAAATTATAAA
Found at i:38851848 original size:31 final size:29
Alignment explanation
Indices: 38851814--38851915 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 29
38851804 TAAATATACT
*
38851814 AATTTGGTACTTATGTTTGGTTTCAATGTTT
1 AATTTGGTACTTA-GTTT-GTTTCAATGTTC
* *
38851845 AATTTAGTACTTAAGTTT-TTT--TTGTCTC
1 AATTTGGTACTT-AGTTTGTTTCAATGT-TC
*
38851873 AATTTGGTACTTGAGTTTAGCTTCAATGTTC
1 AATTTGGTACTT-AGTTT-GTTTCAATGTTC
38851904 AATTTGGTACTT
1 AATTTGGTACTT
38851916 GAATTTTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.05
28 17 0.29
29 3 0.05
30 2 0.03
31 29 0.50
32 4 0.07
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.52
Consensus pattern (29 bp):
AATTTGGTACTTAGTTTGTTTCAATGTTC
Found at i:38852830 original size:35 final size:33
Alignment explanation
Indices: 38852774--38852839 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 33
38852764 TCTAAATATG
*
38852774 TTACGATTAGTAATCTGATTATGCTTTATAATACA
1 TTACAATTAGTAATCTGATTATG-TTTA-AATACA
*
38852809 TTACAATTATTAATCTGATTATGTTTAAATA
1 TTACAATTAGTAATCTGATTATGTTTAAATA
38852840 TCTATTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 4 0.14
35 21 0.72
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (33 bp):
TTACAATTAGTAATCTGATTATGTTTAAATACA
Found at i:38853852 original size:2 final size:2
Alignment explanation
Indices: 38853845--38853871 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38853835 TATCACTTTG
38853845 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
38853872 ATCTATCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38862244 original size:21 final size:20
Alignment explanation
Indices: 38862220--38862267 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
38862210 AGAAGAGAAT
38862220 AGAAAATAAAGAGAAAAAAAA
1 AGAAAATAAAG-GAAAAAAAA
* * *
38862241 AGAAAGTTAAAGGAACATAAA
1 AGAAA-ATAAAGGAAAAAAAA
38862262 AGAAAA
1 AGAAAA
38862268 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (20 bp):
AGAAAATAAAGGAAAAAAAA
Found at i:38867519 original size:8 final size:8
Alignment explanation
Indices: 38867506--38867530 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38867496 TATACTAAAC
38867506 AATAAAAT
1 AATAAAAT
38867514 AATAAAAT
1 AATAAAAT
38867522 AATAAAAT
1 AATAAAAT
38867530 A
1 A
38867531 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:38868157 original size:22 final size:22
Alignment explanation
Indices: 38868130--38868176 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38868120 TTTTAATGAC
* *
38868130 ATTTTTAATGCATTAAGTTTAA
1 ATTTTTAATGCAATAAGTATAA
*
38868152 ATTTTTCATGCAATAAGTATAA
1 ATTTTTAATGCAATAAGTATAA
38868174 ATT
1 ATT
38868177 CACGTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTTTAATGCAATAAGTATAA
Found at i:38870242 original size:5 final size:5
Alignment explanation
Indices: 38870232--38870258 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38870222 TACGAAGTGT
38870232 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
38870259 ACAGATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:38871205 original size:16 final size:15
Alignment explanation
Indices: 38871171--38871215 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
38871161 AAATAATTTA
*
38871171 AAATTTAAA--AATC
1 AAATTTAAACTAATT
38871184 AAATTTAAACTACATT
1 AAATTTAAACTA-ATT
38871200 AAATTTAAACTAATT
1 AAATTTAAACTAATT
38871215 A
1 A
38871216 GAGAGTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.32
15 5 0.18
16 14 0.50
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTAAACTAATT
Found at i:38884583 original size:23 final size:23
Alignment explanation
Indices: 38884557--38884625 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
38884547 TGAAAGTAAT
38884557 TTAAAATAATAGGTGAACTGTCA
1 TTAAAATAATAGGTGAACTGTCA
* * *
38884580 TT--AA-ACTA--TGAA-AGTAA
1 TTAAAATAATAGGTGAACTGTCA
38884597 TTTAAAATAATAGGTGAACTGTCA
1 -TTAAAATAATAGGTGAACTGTCA
38884621 TTAAA
1 TTAAA
38884626 CTATTAGCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
20 5 0.15
21 5 0.15
23 11 0.33
24 3 0.09
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (23 bp):
TTAAAATAATAGGTGAACTGTCA
Found at i:38884603 original size:41 final size:41
Alignment explanation
Indices: 38884546--38884629 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
38884536 AAATCCTAAC
38884546 ATGAAAGTAATTTAAAATAATAGGTGAACTGTCATTAAACT
1 ATGAAAGTAATTTAAAATAATAGGTGAACTGTCATTAAACT
38884587 ATGAAAGTAATTTAAAATAATAGGTGAACTGTCATTAAACT
1 ATGAAAGTAATTTAAAATAATAGGTGAACTGTCATTAAACT
38884628 AT
1 AT
38884630 TAGCAAAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (41 bp):
ATGAAAGTAATTTAAAATAATAGGTGAACTGTCATTAAACT
Found at i:38888683 original size:23 final size:23
Alignment explanation
Indices: 38888645--38888695 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
38888635 CCAATGTCGT
* *
38888645 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
38888668 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
38888691 AGTAA
1 TGTAA
38888696 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:38892433 original size:59 final size:61
Alignment explanation
Indices: 38892366--38892483 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 61
38892356 TGATTAAACT
* * *
38892366 TAATCACTTTAATAATAAATTAATATAATA-TTAA-TATTAGATTAAATTTAATATTAAGA
1 TAATCACTTTAATAATAAATTAATAAAATAGATAAGTATTAAATTAAATTTAATATTAAGA
* *
38892425 TAATCACTTTAATATTAAATTAATAAAATAGATAAGTATTAAATTTAATTTAATATTAA
1 TAATCACTTTAATAATAAATTAATAAAATAGATAAGTATTAAATTAAATTTAATATTAA
38892484 ACTATTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 28 0.54
60 3 0.06
61 21 0.40
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (61 bp):
TAATCACTTTAATAATAAATTAATAAAATAGATAAGTATTAAATTAAATTTAATATTAAGA
Found at i:38892791 original size:13 final size:13
Alignment explanation
Indices: 38892775--38892818 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
38892765 TTTTTCAAGA
38892775 AAATTCCTTAATC
1 AAATTCCTTAATC
* * *
38892788 AAATTCCTGAGTT
1 AAATTCCTTAATC
*
38892801 AAATTCTTTAATC
1 AAATTCCTTAATC
38892814 AAATT
1 AAATT
38892819 ATTTAGTTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (13 bp):
AAATTCCTTAATC
Found at i:38895641 original size:23 final size:23
Alignment explanation
Indices: 38895614--38895666 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
38895604 AATGTTATTG
38895614 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
38895637 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38895660 ATCAGTG
1 ATCAGTG
38895667 TGGCAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38897407 original size:5 final size:5
Alignment explanation
Indices: 38897397--38897424 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38897387 TTACTTAGCC
38897397 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
38897425 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:38899620 original size:15 final size:15
Alignment explanation
Indices: 38899600--38899629 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38899590 CTATGCATGC
*
38899600 AAAATATAAAAGACA
1 AAAATACAAAAGACA
38899615 AAAATACAAAAGACA
1 AAAATACAAAAGACA
38899630 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:38902468 original size:53 final size:53
Alignment explanation
Indices: 38902410--38902517 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
38902400 ATGTCATGTT
*
38902410 TACATGGACCGATTATTTAATTAATAGAAGAAGTACAAGATTATTTAACTACA
1 TACATGGACCGATTATTTAATTAATAGAAGAAGTACAAGAATATTTAACTACA
*
38902463 TACATGGACCGATTATTTAATTAGTAGAAGAAGTACAAGAATATTTAACTACA
1 TACATGGACCGATTATTTAATTAATAGAAGAAGTACAAGAATATTTAACTACA
38902516 TA
1 TA
38902518 AACAATATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (53 bp):
TACATGGACCGATTATTTAATTAATAGAAGAAGTACAAGAATATTTAACTACA
Found at i:38904726 original size:22 final size:23
Alignment explanation
Indices: 38904701--38904746 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
38904691 CCATTCAATG
* *
38904701 TTCAGTTTGGTACTT-GAGTTTT
1 TTCAATTTGATACTTCGAGTTTT
*
38904723 TTCAATTTGATATTTCGAGTTTT
1 TTCAATTTGATACTTCGAGTTTT
38904746 T
1 T
38904747 CTTTATCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (23 bp):
TTCAATTTGATACTTCGAGTTTT
Found at i:38910509 original size:12 final size:11
Alignment explanation
Indices: 38910492--38910527 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
38910482 AACAAATCCT
38910492 CTCTCATATTTC
1 CTCTCA-ATTTC
*
38910504 CTCTCAATTTT
1 CTCTCAATTTC
38910515 CTCTCAATTTC
1 CTCTCAATTTC
38910526 CT
1 CT
38910528 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:38910538 original size:22 final size:23
Alignment explanation
Indices: 38910491--38910539 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
38910481 AAACAAATCC
**
38910491 TCTCTCATATTTCCTCTCAATTT
1 TCTCTCATATTTCCTCTCAAAAT
38910514 TCTCTCA-ATTTCCT-TCCAAAAT
1 TCTCTCATATTTCCTCT-CAAAAT
38910536 TCTC
1 TCTC
38910540 ATAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCTCATATTTCCTCTCAAAAT
Found at i:38910583 original size:51 final size:51
Alignment explanation
Indices: 38910507--38910627 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
38910497 ATATTTCCTC
* * * *
38910507 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATAATTAATA
1 TCAATTTACTCTCAATTTCATTCCAAAAATCTC-TCAAAGCCATAATTAATA
* *
38910558 TCAATTTACTCTCAATTTCATTCCAAAAATCTCTCAAAGCCATATTTAATT
1 TCAATTTACTCTCAATTTCATTCCAAAAATCTCTCAAAGCCATAATTAATA
*
38910609 TCAATTTGCTCTCAATTTC
1 TCAATTTACTCTCAATTTC
38910628 CTTTTTTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (51 bp):
TCAATTTACTCTCAATTTCATTCCAAAAATCTCTCAAAGCCATAATTAATA
Found at i:38911757 original size:7 final size:7
Alignment explanation
Indices: 38911741--38911772 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38911731 TGCAAATAGA
*
38911741 TATTTTG
1 TATTTAG
38911748 TATTTAG
1 TATTTAG
38911755 TATTTAG
1 TATTTAG
38911762 TATTTAG
1 TATTTAG
38911769 TATT
1 TATT
38911773 ATGTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:38911778 original size:14 final size:13
Alignment explanation
Indices: 38911744--38911778 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
38911734 AAATAGATAT
38911744 TTTGTATTTAGTA
1 TTTGTATTTAGTA
38911757 TTTAGTATTTAGTA
1 TTT-GTATTTAGTA
38911771 TTATGTAT
1 TT-TGTAT
38911779 ATAACTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTGTATTTAGTA
Found at i:38912431 original size:18 final size:18
Alignment explanation
Indices: 38912404--38912443 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
38912394 CAGGTGCGTT
*
38912404 TCCTATCCCTTATATGTA
1 TCCTAACCCTTATATGTA
38912422 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
38912440 TCCT
1 TCCT
38912444 TTTCCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:38912897 original size:25 final size:25
Alignment explanation
Indices: 38912868--38912916 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38912858 TTAATATTTT
*
38912868 GAAGTTTGT-TTGATGTAATAAAATA
1 GAAGTTT-TATTGATGTAAAAAAATA
38912893 GAAGTTTTATTGATGTAAAAAAAT
1 GAAGTTTTATTGATGTAAAAAAAT
38912917 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (25 bp):
GAAGTTTTATTGATGTAAAAAAATA
Found at i:38912980 original size:25 final size:25
Alignment explanation
Indices: 38912949--38913229 Score: 191
Period size: 25 Copynumber: 11.6 Consensus size: 25
38912939 TTGATATTAT
38912949 TTGATGTAATAAAATAGAAGTTTTA
1 TTGATGTAATAAAATAGAAGTTTTA
** * *
38912974 TTGATGTAATAAAAATTTAAATTTTT
1 TTGATGTAAT-AAAATAGAAGTTTTA
** * *
38913000 TTGA-GT--T-ATTTTG-A-TATTA
1 TTGATGTAATAAAATAGAAGTTTTA
38913019 TTTGATGTAATAAAATAGAAG-TTTA
1 -TTGATGTAATAAAATAGAAGTTTTA
38913044 TTTGATGTAATAAAATAGAAG-TTTA
1 -TTGATGTAATAAAATAGAAGTTTTA
38913069 TATGATGTAATAAAATAGAAGTTTTA
1 T-TGATGTAATAAAATAGAAGTTTTA
** * *
38913095 TTGATGTAATAAAAATTTAAATTTTT
1 TTGATGTAAT-AAAATAGAAGTTTTA
** * *
38913121 TTGA-GT--T-ATTTTG-A-TATTA
1 TTGATGTAATAAAATAGAAGTTTTA
*
38913140 TTTGATGTAATAAAATATAAG-TTTA
1 -TTGATGTAATAAAATAGAAGTTTTA
*
38913165 TTTGATGTAATAAAATAGATG-TTTA
1 -TTGATGTAATAAAATAGAAGTTTTA
38913190 TATGATGTAATAAAATAGAAG-TTTA
1 T-TGATGTAATAAAATAGAAGTTTTA
*
38913215 TTTGATGTGATAAAA
1 -TTGATGTAATAAAA
38913230 ATTGAAAACC
Statistics
Matches: 205, Mismatches: 31, Indels: 40
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.03
20 10 0.05
21 10 0.05
23 4 0.02
24 7 0.03
25 132 0.64
26 36 0.18
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.44
Consensus pattern (25 bp):
TTGATGTAATAAAATAGAAGTTTTA
Found at i:38913029 original size:71 final size:72
Alignment explanation
Indices: 38912876--38913058 Score: 327
Period size: 71 Copynumber: 2.6 Consensus size: 72
38912866 TTGAAGTTTG
38912876 TTTGATGTAATAAAATAGAAGTTTTATTGATGTAA-AAAAATTTTTAAATTTTTTTGAGTTATTT
1 TTTGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAA-TTTTAAATTTTTTTGAGTTATTT
38912940 TGATATTA
65 TGATATTA
38912948 TTTGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAA-TTTAAATTTTTTTGAGTTATTTT
1 TTTGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTTAAATTTTTTTGAGTTATTTT
38913012 GATATTA
66 GATATTA
38913019 TTTGATGTAATAAAATAGAAG-TTTATTTGATGTAATAAAA
1 TTTGATGTAATAAAATAGAAGTTTTA-TTGATGTAATAAAA
38913059 TAGAAGTTTA
Statistics
Matches: 109, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
70 4 0.04
71 65 0.60
72 35 0.32
73 5 0.05
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (72 bp):
TTTGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTTAAATTTTTTTGAGTTATTTT
GATATTA
Found at i:38913075 original size:121 final size:121
Alignment explanation
Indices: 38912945--38913232 Score: 524
Period size: 121 Copynumber: 2.4 Consensus size: 121
38912935 TATTTTGATA
*
38912945 TTATTTGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAGTTATT
1 TTATATGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAGTTATT
38913010 TTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAGT
66 TTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAGT
38913066 TTATATGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAGTTATT
1 TTATATGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAGTTATT
* *
38913131 TTGATATTATTTGATGTAATAAAATATAAGTTTATTTGATGTAATAAAATAGATGT
66 TTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAGT
*
38913187 TTATATGATGTAATAAAATAGAAG-TTTATTTGATGTGATAAAAATT
1 TTATATGATGTAATAAAATAGAAGTTTTA-TTGATGTAATAAAAATT
38913233 GAAAACCCTA
Statistics
Matches: 162, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
120 4 0.02
121 158 0.98
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (121 bp):
TTATATGATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAGTTATT
TTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAGT
Found at i:38913261 original size:23 final size:23
Alignment explanation
Indices: 38913231--38913838 Score: 743
Period size: 23 Copynumber: 25.7 Consensus size: 23
38913221 GTGATAAAAA
38913231 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
* *
38913254 TTGAAAACCGTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
*
38913277 TTAAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913300 TTGAAAACCCTAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
* * *
38913323 TTGAAAACCTTAACTTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
38913346 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913369 TTGAAAACCCAAAACCCTAACCTAATTAAA
1 TTG-------AAAACCCTAACCTAATTAAG
*
38913399 TTGAAAACCCTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
*
38913422 TTGAAAACCCTAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913445 TTGAAAACCCTAACATAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
38913468 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913491 TTGAAAACCCTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
* *
38913514 TTAAAAACCGTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913537 TTGAAAACCCTAACCTAATTCTAAC
1 TTGAAAACCCTAACCTAA-T-TAAG
* **
38913562 CT-AATTAA-GTTGAAAACCCTAACCTAATTAAG
1 TTGAA--AACCCT---AA-CCT-A----ATTAAG
*
38913594 TTGAAAACCCCAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913617 TTGAAAACCCTAACCTAATTAAC
1 TTGAAAACCCTAACCTAATTAAG
* *
38913640 TTAAAAACCCTAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
38913663 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913686 TTGAAAACCCTAACCTAATTAAC
1 TTGAAAACCCTAACCTAATTAAG
* *
38913709 TTAAAAACCCTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
* *
38913732 TTAAAAACCCTAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913755 TTGAAAACCCTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
* *
38913778 TTAAAAACCCTAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
38913801 TTGAAAACCTTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
38913824 TTGAAAACCCTAACC
1 TTGAAAACCCTAACC
38913839 CTAAACTTAA
Statistics
Matches: 508, Mismatches: 55, Indels: 44
0.84 0.09 0.07
Matches are distributed among these distances:
23 454 0.89
24 3 0.01
25 5 0.01
26 2 0.00
27 1 0.00
28 5 0.01
29 5 0.01
30 23 0.05
31 2 0.00
32 4 0.01
33 3 0.01
34 1 0.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (23 bp):
TTGAAAACCCTAACCTAATTAAG
Found at i:38913284 original size:46 final size:46
Alignment explanation
Indices: 38913228--38913838 Score: 823
Period size: 46 Copynumber: 13.4 Consensus size: 46
38913218 GATGTGATAA
*
38913228 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCGTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913274 AAATTAAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTATTT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* * * *
38913320 AAGTTGAAAACCTTAACTTATTTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913366 AAGTTGAAAACCCAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATT
1 AAATTG-------AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913419 AAATTGAAAACCCTAACCTATTTAAGTTGAAAACCCTAACATAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
*
38913465 AAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913511 AAATTAAAAACCGTAACCTAATTAAGTTGAAAACCCTAACC----T
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
38913553 -AATT-------CTAACCTAATTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913591 AAGTTGAAAACCCCAACCTAATTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* * *
38913637 AACTTAAAAACCCTAACCTATTTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* * *
38913683 AAGTTGAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* *
38913729 AAATTAAAAACCCTAACCTATTTAAGTTGAAAACCCTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
* * *
38913775 AAATTAAAAACCCTAACCTATTTAAGTTGAAAACCTTAACCTAATT
1 AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
*
38913821 AAGTTGAAAACCCTAACC
1 AAATTGAAAACCCTAACC
38913839 CTAAACTTAA
Statistics
Matches: 503, Mismatches: 43, Indels: 38
0.86 0.07 0.07
Matches are distributed among these distances:
34 28 0.06
38 1 0.00
39 3 0.01
41 4 0.01
42 1 0.00
46 425 0.84
53 41 0.08
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (46 bp):
AAATTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATT
Found at i:38913353 original size:69 final size:69
Alignment explanation
Indices: 38913231--38913838 Score: 826
Period size: 69 Copynumber: 8.9 Consensus size: 69
38913221 GTGATAAAAA
* * *
38913231 TTGAAAACCCTAACCTAATTAAGTTGAAAACCGTAACCTAATTAAATTAAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
38913296 TAAG
66 TAAG
* * * *
38913300 TTGAAAACCCTAACCTATTTAAGTTGAAAACCTTAACTTATTTAAGTTGAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
38913365 TAAG
66 TAAG
* *
38913369 TTGAAAACCCAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTGAAAACCCTA
1 TTG-------AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTA
*
38913434 ACCTATTTAAG
59 ACCTAATTAAG
*
38913445 TTGAAAACCCTAACATAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
*
38913510 TAAA
66 TAAG
* *
38913514 TTAAAAACCGTAACCTAATTAAGTTGAAAACCCTAACC----TAA-TT-------CTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
38913567 TAAG
66 TAAG
*
38913571 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCCAACCTAATTAAGTTGAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
*
38913636 TAAC
66 TAAG
* *
38913640 TTAAAAACCCTAACCTATTTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
*
38913705 TAAC
66 TAAG
* * * *
38913709 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTATTTAAGTTGAAAACCCTAACCTAAT
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
*
38913774 TAAA
66 TAAG
* * *
38913778 TTAAAAACCCTAACCTATTTAAGTTGAAAACCTTAACCTAATTAAGTTGAAAACCCTAACC
1 TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACC
38913839 CTAAACTTAA
Statistics
Matches: 481, Mismatches: 39, Indels: 38
0.86 0.07 0.07
Matches are distributed among these distances:
57 48 0.10
61 3 0.01
62 2 0.00
64 2 0.00
65 3 0.01
69 361 0.75
76 62 0.13
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (69 bp):
TTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTAAT
TAAG
Found at i:38913383 original size:30 final size:30
Alignment explanation
Indices: 38913349--38913408 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
38913339 ATTTAAGTTG
*
38913349 AAAACCCTAACCTAATTAAGTTGAAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCC
38913379 AAAACCCTAACCTAATTAAATTGAAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCC
38913409 TAACCTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.20
Consensus pattern (30 bp):
AAAACCCTAACCTAATTAAATTGAAAACCC
Found at i:38913567 original size:34 final size:34
Alignment explanation
Indices: 38913524--38913590 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
38913514 TTAAAAACCG
38913524 TAACCTAATTAAGTTGAAAACCCTAACCTAATTC
1 TAACCTAATTAAGTTGAAAACCCTAACCTAATTC
38913558 TAACCTAATTAAGTTGAAAACCCTAACCTAATT
1 TAACCTAATTAAGTTGAAAACCCTAACCTAATT
38913591 AAGTTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (34 bp):
TAACCTAATTAAGTTGAAAACCCTAACCTAATTC
Found at i:38917322 original size:125 final size:124
Alignment explanation
Indices: 38917092--38917331 Score: 367
Period size: 125 Copynumber: 1.9 Consensus size: 124
38917082 CCCAAACAGG
* * *
38917092 CTACTGTAGCAAAAGCGCGTCCCCAAGGGTGCGATTTTCACAAATTCTTCTCAAATAGCATCTTG
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
38917157 CTAGAAGCGAATTTATACTATTTGCTCAGAAACGTAAAAAAAAAATTATTTCATCCATGAC
66 CTAGAAGCGAATTTATACTATTTGCTCAGAAACGT--AAAAAAAATTATTTCATCCATGAC
* *
38917218 CTACTGTAGCAAGAGCGCGTCCACGAGGGCGCGA-TTTCA-AAATTTCTTCTCAAATAGCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTTCACAAA-TTCTTCTCAAATAGCATCCT
* * *
38917281 GCTAGAAGCGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAATTATTTC
65 GCTAGAAGCGAATTTATACTATTTGCTCAGAAACGTAAAAAAAATTATTTC
38917332 TTCCCAGACC
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
123 14 0.13
124 3 0.03
125 58 0.55
126 30 0.29
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
CTAGAAGCGAATTTATACTATTTGCTCAGAAACGTAAAAAAAATTATTTCATCCATGAC
Found at i:38917370 original size:7 final size:7
Alignment explanation
Indices: 38917358--38917384 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38917348 CCTTAAAAAG
38917358 CCTAAAC
1 CCTAAAC
38917365 CCTAAAC
1 CCTAAAC
38917372 CCTAAAC
1 CCTAAAC
38917379 CCTAAA
1 CCTAAA
38917385 AGCCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:38918312 original size:13 final size:13
Alignment explanation
Indices: 38918294--38918322 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38918284 TTATTGAAAA
38918294 TCTGTTGAAGATT
1 TCTGTTGAAGATT
38918307 TCTGTTGAAGATT
1 TCTGTTGAAGATT
38918320 TCT
1 TCT
38918323 TCTTCTCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (13 bp):
TCTGTTGAAGATT
Found at i:38929472 original size:41 final size:42
Alignment explanation
Indices: 38929388--38929480 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
38929378 TTCTGTGGGA
* * *
38929388 AAACGCCGCTATAAAACATGATCTTTAGCGGTGCTTTTATTAC
1 AAACGCTGCTAAAAAACATGATCTTTAGCGAT-CTTTTATTAC
* * *
38929431 AAATGCTGCTAAAAAACATGATTTTTAGCGAT-TTTTTTTAC
1 AAACGCTGCTAAAAAACATGATCTTTAGCGATCTTTTATTAC
38929472 AAACGCTGC
1 AAACGCTGC
38929481 AAGAGAGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 16 0.37
43 27 0.63
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (42 bp):
AAACGCTGCTAAAAAACATGATCTTTAGCGATCTTTTATTAC
Found at i:38937116 original size:23 final size:23
Alignment explanation
Indices: 38937086--38937129 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
38937076 AACAATTTGC
38937086 AAATATAGGACAATGAAGGCTTT
1 AAATATAGGACAATGAAGGCTTT
38937109 AAATATAGGACAATGAAGGCT
1 AAATATAGGACAATGAAGGCT
38937130 ATAAGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (23 bp):
AAATATAGGACAATGAAGGCTTT
Found at i:38943686 original size:19 final size:21
Alignment explanation
Indices: 38943648--38943701 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
38943638 GTTGAAAATG
38943648 ATATTTATTTAATATAAATTT
1 ATATTTATTTAATATAAATTT
*
38943669 ATATTTA-TT-ATTTAAATTT
1 ATATTTATTTAATATAAATTT
*
38943688 -T-TTTATATAATATA
1 ATATTTATTTAATATA
38943702 TAAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 13 0.46
20 2 0.07
21 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTATTTAATATAAATTT
Found at i:38944235 original size:5 final size:6
Alignment explanation
Indices: 38944218--38944242 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38944208 TAAATAACTT
38944218 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
38944243 CTCTATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:38946150 original size:27 final size:24
Alignment explanation
Indices: 38946104--38946153 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
38946094 AGATGAAATT
*
38946104 TTTAATTAAAAAATTTATTTTTTA
1 TTTAATTAAAAAATTAATTTTTTA
*
38946128 TTTAATATATAAAAATTAAATTTTTA
1 TTTAAT-TA-AAAAATTAATTTTTTA
38946154 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAATTAAAAAATTAATTTTTTA
Found at i:38948819 original size:24 final size:24
Alignment explanation
Indices: 38948786--38948849 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
38948776 AAACCTAATT
* * *
38948786 CTAATCAATGTTAAATATATTATG
1 CTAATAAATGCTAAATATATTATA
38948810 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
* *
38948834 CCAATAAATACTAAAT
1 CTAATAAATGCTAAAT
38948850 CTTCTAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:38957226 original size:16 final size:17
Alignment explanation
Indices: 38957205--38957242 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
38957195 CCATTCCTTT
38957205 CACACCCTCGTCA-CCC
1 CACACCCTCGTCACCCC
38957221 CACACCCTCGTCACCCC
1 CACACCCTCGTCACCCC
38957238 CACAC
1 CACAC
38957243 AACCCTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.21, C:0.63, G:0.05, T:0.11
Consensus pattern (17 bp):
CACACCCTCGTCACCCC
Found at i:38957932 original size:23 final size:23
Alignment explanation
Indices: 38957905--38957951 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
38957895 ATTAGGGGAG
*
38957905 AAAATTAACGAATTTTGAGGGTT
1 AAAATTAAAGAATTTTGAGGGTT
*
38957928 AAAATTAAAGAATTTTGGGGGTT
1 AAAATTAAAGAATTTTGAGGGTT
38957951 A
1 A
38957952 TCGGGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (23 bp):
AAAATTAAAGAATTTTGAGGGTT
Found at i:38960905 original size:6 final size:6
Alignment explanation
Indices: 38960882--38960924 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
38960872 GAATTATTTT
* * *
38960882 TTTTAT TTTTAG ACTTTAG TTTTAG TTTTCG TTTTAG TTTTAG
1 TTTTAG TTTTAG -TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
38960925 AATTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.65
Consensus pattern (6 bp):
TTTTAG
Done.